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In the context of sensing and transport control, nanopores play an essential role. Designing multifunctional nanopores and placing multiple surface functionalities with nanoscale precision remains challenging. Interface effects together with a combination of different materials are used to obtain local multifunctionalization of nanoscale pores within a model pore system prepared by colloidal templating. Silica inverse colloidal monolayers are first functionalized with a gold layer to create a hybrid porous architecture with two distinct gold nanostructures on the top surface as well as at the pore bottom. Using orthogonal silane- and thiol-based chemistry together with a control of the wetting state allows individual addressing of the different locations within each pore resulting in nanoscale localized functional placement of three different functional units. Ring-opening metathesis polymerization is used for inner silica-pore wall functionalization. The hydrophobized pores create a Cassie–Baxter wetting state with aqueous solutions of thiols, which enables an exclusive functionalization of the outer gold structures. In a third step, an ethanolic solution able to wet the pores is used to self-assemble a thiol-containing initiator at the pore bottom. Subsequent controlled radical polymerization provides functionalization of the pore bottom. It is demonstrated that the combination of orthogonal surface chemistry and controlled wetting states can be used for the localized functionalization of porous materials.